Feeback On Upgrades:
Unused ship upgrades from anomalies do not stack. This ends up (perhaps counter-intuitively) encouraging me to delay upgrading ships because if I don't have an upgrade slot to use those juicy anomaly upgrades on, then I risk losing out on upgrades. And it's not at all clear that this is intended or not.
Now, if this is intended in order to make me choose between upgrading to avoid losing out on combat/utility now or keeping my ships abilities lower for now "just in case" I might get a more powerful upgrade, that's ok. But if this is the intended gameplay loop for these upgrades, please communicate via tooltip on the anomaly popup whether or not I already have a copy of that upgrade stored for later use. And ideally also communicate somehow in that same space or in the ship upgrade menu that I can only store one of each of the "free" anomaly upgrades.
If this is not an intended gameplay choice, then the Ship Upgrades menu should have an indicator on the corner of the icon for each limited-quantity upgrade indicating how many I have in stock. For the resource-dependent upgrades, the number could show how many I'm currently able to build.
The available quantity of these should be treated in a similar fashion as ship upgrades, with an numeric indicator on the upgrade menu icon of how many of them I have stored. For the ones where I can build as many of them as I like, provided I have the nanobots, either an infinity icon or a quantity currently able to build would be great to see.